fo40225

wget https://github.com/seaweedfs/seaweedfs/releases/download/3.73/linux_amd64.tar.gz
tar axvf linux_amd64.tar.gz
rm linux_amd64.tar.gz

sudo mv weed /usr/local/bin

sudo mkdir -p /usr/local/etc/seaweedfs
sudo chown user:user /usr/local/etc/seaweedfs
weed scaffold -config=master > /usr/local/etc/seaweedfs/master.toml

fo40225

echo | {} -dM -E - | grep clang_version

#define __clang_version__ "12.0.0 (icx 2020.10.0.1113)"
#define __clang_version__ "12.0.0 (icx 2021.2.0.20210317)"
#define __clang_version__ "13.0.0 (icx 2021.3.0.20210619)"
#define __clang_version__ "13.0.0 (icx 2021.4.0.20210924)"
#define __clang_version__ "14.0.0 (icx 2022.0.0.20211123)"
#define __clang_version__ "14.0.0 (icx 2022.0.0.20211123)"
#define __clang_version__ "14.0.0 (icx 2022.1.0.20220316)"
#define __clang_version__ "15.0.0 (icx 2022.2.0.20220730)"

fo40225

options(timeout = 10)
cranometer <- function(ms = getCRANmirrors(all = FALSE, local.only = FALSE),...){
   dest = tempfile()
   
   nms = dim(ms)[1]
   ms$t = rep(NA,nms)
   for(i in 1:nms){
      m = ms[i,]
      url = paste(m$URL,"src/base/NEWS",sep="")
      t = try(system.time(download.file(url,dest),gcFirst=TRUE))

fo40225

# cgroups v1 (ubuntu <=20.04)
sudo docker run --name centos-1 --restart unless-stopped -i -t -d -p 2222:22 --privileged --stop-signal SIGRTMIN+3 --entrypoint /usr/sbin/init --tmpfs /run -v /sys/fs/cgroup:/sys/fs/cgroup:ro -v /var/run/docker.sock:/var/run/docker.sock centos:7.9.2009
sudo docker run --name ubuntu-1 --restart unless-stopped -i -t -d -p 2222:22 --privileged --stop-signal SIGRTMIN+3 --entrypoint /sbin/init --tmpfs /run -v /sys/fs/cgroup:/sys/fs/cgroup:ro -v /var/run/docker.sock:/var/run/docker.sock ubuntu:16.04
sudo docker run --name debian-1 --restart unless-stopped -i -t -d -p 2222:22 --privileged --stop-signal SIGRTMIN+3 --entrypoint /sbin/init --tmpfs /run -v /sys/fs/cgroup:/sys/fs/cgroup:ro -v /var/run/docker.sock:/var/run/docker.sock debian:8.11

# cgroups v2 (ubuntu >=22.04)
sudo docker run --name rhel-1 --restart unless-stopped -i -t -d -p 2222:22 --privileged -v /var/run/docker.sock:/var/run/docker.sock redhat/ubi8-init:8.10
sudo docker run --name rhel-1 --restart unless-stopped -i -t -d 

fo40225

pip install biopython==1.78
sudo apt install -y prodigal

# PATH need contain diamond, blast, kma, samtools, bamtools, bedtools2

git clone https://github.com/arpcard/rgi.git -b 6.0.1

cd rgi

# app/Diamond.py

fo40225

cd ~
git clone https://github.com/DerrickWood/kraken2.git -b v2.1.2
cd kraken2/

./install_kraken2.sh bin

~/kraken2/bin/kraken2-build --download-taxonomy --protein --db db_protein
#~/kraken2/bin/kraken2-build --download-library human --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library archaea --protein --db db_protein
~/kraken2/bin/kraken2-build --download-library bacteria --protein --db db_protein

fo40225

import re
import urllib.request
import pandas as pd
from io import BytesIO
from zipfile import ZipFile
from IPython.display import display
import matplotlib.pyplot as plt
import numpy as np

datas = pd.DataFrame(columns=[

fo40225

wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_15/gencode.v15.annotation.gtf.gz
wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_21/gencode.v21.chr_patch_hapl_scaff.annotation.gtf.gz

gunzip gencode.v15.annotation.gtf.gz
gunzip gencode.v21.chr_patch_hapl_scaff.annotation.gtf.gz

grep exon gencode.v15.annotation.gtf \
 |awk '{printf("%s\t%s\t%s\n",$1,int($4)-1,$5);}' |sort -T . -k1,1 -k2,2n | bedtools merge > gencode.37.bed
grep exon gencode.v21.chr_patch_hapl_scaff.annotation.gtf \
 |awk '{printf("%s\t%s\t%s\n",$1,int($4)-1,$5);}' |sort -T . -k1,1 -k2,2n | bedtools merge > gencode.38.bed

fo40225

https://repo.msys2.org/distrib/x86_64/

msys2-x86_64-20150916 5.2.0-3

msys2-x86_64-20160205 5.3.0-1

msys2-x86_64-20160921 6.1.0-1

msys2-x86_64-20161025 6.2.0-2

fo40225

git clone https://github.com/seppinho/mutserve.git -b v1.3.4
wget https://github.com/seppinho/mutserve/releases/download/v1.3.4/mutserve-1.3.4.jar

export ref=mutserve/files/rCRS.fasta

bwa index $ref

bwa mem -M -t 4 $ref mt_R1.fq.gz mt_R2.fq.gz \
| samtools view -@ 4 -1 -o mt.bam